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At least 649 records · Page 36Linked to original sources

The tef1 box, a ubiquitous cis-acting element involved in the activation of plant genes that are highly expressed in cycling cells.

In Arabidopsis thaliana, the tef1 box is a cis-acting promoter element of the EF-1 alpha A1 gene involved in the activation of transcription in meristematic tissues. The initiation of root calli in transgenic Arabidopsis by 2,4-D shows that the tef1-dependent expression of the GUS reporter gene is not restricted to meristematic regions but involves all of the cycling cells. Hybridization experiments conducted using Arabidopsis cDNA clones organized in a dense array on filters, and cDNA probes prepared from cells in various states of growth, or blocked at different steps of the cell cycle, indicate that the enhanced expression of EF-1 alpha genes occurs in cycling cells at the point of entry into the cell cycle and remains constant during transit through the cycle. The analysis of several promoters of genes, other than EF-1 alpha, which are overexpressed in growing cells and involved in the processes of translation or redox regulation, reveals the presence of sequences showing partial homologies with the tef1 box. The Arabidopsis ribosomal gene srp18 and the tobacco gene thioh2, encoding a thioredoxin h, contain such sequences. Gel retardation experiments suggest that these sequences are targets for the same proteins as those that interact with the tef1 box of the Arabidopsis EF-1 alpha A1 gene. In transfected Arabidopsis protoplasts, the putative tef1 sequence thioh2 partially restores the activity of a tef1 box-less EF-1 alpha A1 promoter. These data demonstrate that the tef1 box is a ubiquitous cis-acting element involved in the transcriptional activation of plant genes that are overexpressed in cycling cells.(ABSTRACT TRUNCATED AT 250 WORDS)

Aphidicolin↗

Identification of the region in Escherichia coli DnaA protein required for specific recognition of the DnaA box.

DnaA protein binds specifically to a 9-base- pair motif called the DnaA box. Domain IV comprises 94 amino acid residues and is required for DNA binding. Using nuclear magnetic resonance analysis, we investigated the interaction between DnaA domain IV and both a DnaA box and a non-specific oligonucleotide that has a reduced affinity for DnaA. The 1H-15N HSQC spectrum of DnaA domain IV showed prominent chemical shift perturbations on six residues (Arg399, Ala404, Leu422, Asp433, Thr435 and Thr436) in the presence of the DnaA box. Through homology modeling, we located all of these residues on one side surface of the DnaA domain IV molecule. Moreover, we compared the chemical shift perturbation of the 1H-15N HSQC spectrum in the presence of the DnaA box with that in the presence of a non-specific oligonucleotide, and the results suggested that Leu422 imparts specificity in binding with the DnaA box.

Amino Acid Sequence↗

MADS box genes in oil palm (Elaeis guineensis): patterns in the evolution of the SQUAMOSA, DEFICIENS, GLOBOSA, AGAMOUS, and SEPALLATA subfamilies.

MADS box genes code for a large family of transcription factors which regulate development in higher plants, notably flower formation. We describe here a study of members of the MADS box gene family in oil palm (Elaeis guineensis Jacq.), a representative of the family Arecaceae and order Arecales, a key group of monocotyledons which has been unreported in previous phylogenetic reconstructions of the different recognized clades of MADS box genes. In this study, 13 oil palm MADS box genes were identified and characterized. They were found to belong to five different subfamilies, namely, the previously defined SQUAMOSA, AGAMOUS, AGAMOUS-like2, DEFICIENS, and GLOBOSA groups. Genes belonging to each of these groups play a critical role in the determination of flower structure as defined by the ABCDE model. The in planta expression profiles of the oil palm MADS box genes were studied by RT-PCR and phylogenetic sequence diversity within individual subfamilies was investigated by comparing their deduced protein sequences with those of other angiosperms. Most of the oil palm sequences studied were observed to group with distinct supported clades within their subfamily. Some unexpected groupings were observed between monocot sequences (including oil palm ones) of non-Poaceae origin, probably illustrating the importance of obtaining adequate taxon representation in monocot molecular phylogenies.

Arecaceae↗

A novel endothelial function test using Doppler flow: the snuff-box technique.

Precise measurement of Doppler estimated blood flow volume using the standard technique of flow-mediated vasodilation is not possible because the anatomic course of the brachial or radial artery goes against the principle of Doppler measurements that the insonation angle should be less than 30 degrees . The radial artery in the anatomic snuff-box area is useful for the measurement of Doppler signals as the insonation angle is less than 30 degrees and because the size of the artery allows observation of laminar flow. We introduce the snuff-box technique as a novel endothelial function test that enables measurement of both blood flow and diameter of the radial artery. Changes in diameter and blood flow volume during reactive hyperemia were examined in 15 healthy volunteers. Changes in blood flow determined using the snuff-box technique were compared with changes in forearm blood flow determined by plethysmography. The diameter of the radial artery increased from 2.3 +/- 0.2 mm at baseline to 2.8 +/- 0.4 mm at 60 s after deflation (P = 0.0017), and blood flow increased from 52.3 +/- 21.4 ml/min at baseline to 108.6 +/- 33.1 ml/min at 15 s after deflation (P = 0.0014). Percentile blood flow determined by the snuff-box technique correlated significantly with that determined by plethysmography (r = 0.824, P = 0.0002). Both blood flow volume and artery diameter can be measured with high reliability using the snuff-box technique, as has been shown in subjects with reactive hyperemia.

Adult↗

The ethylene-, jasmonate-, abscisic acid- and NaCl-responsive tomato transcription factor JERF1 modulates expression of GCC box-containing genes and salt tolerance in tobacco.

Ethylene responsive factors (ERFs) are important plant-specific transcription factors, some of which have been demonstrated to interact with the ethylene-responsive GCC box and the dehydration-responsive element (DRE); however, data on the roles of ERF proteins in connection with various signaling pathways are limited. In this research, we used the GCC box, an essential cis-acting element responsive to ethylene and methyl jasmonate (MeJA), as bait in a yeast one-hybrid system to isolate transcription factors from tomato (Lycopersicon esculentum Mill.). One of the cDNAs, which was designated Jasmonate and Ethylene Response Factor 1 (JERF1), encodes an ERF protein, containing a conserved ERF DNA-binding motif and functioning as a transcriptional activator in yeast through targeting to the nucleus in onion (Allium cepa L.) epidermal cells. Biochemical analysis revealed that JERF1 bound not only to the GCC box but also to the DRE sequence. Expression of the JERF1 gene in tomato was induced by ethylene, MeJA, abscisic acid (ABA) and salt treatment, indicating that JERF1 might act as a connector among different signal transduction pathways. Further research with transgenic JERF1 tobacco (Nicotiana tabacum L.) plants indicated that overexpressing JERF1 activated expression of GCC box-containing genes such as osmotin, GLA, Prb-1b and CHN50 under normal growth conditions, and subsequently resulted in enhanced tolerance to salt stress, suggesting that JERF1 modulates osmotic tolerance by activation of downstream gene expression through interaction with the GCC box or DRE.

Abscisic Acid↗

MADS-box gene expression in lateral primordia, meristems and differentiated tissues of Arabidopsis thaliana roots.

Although MADS-box genes involved in flower and fruit development have been well characterized, the function of MADS-box genes expressed in vegetative structures has yet to be explored. At least seven members of this family are grouped in clades of genes that are preferentially expressed in roots of Arabidopsis thaliana (L.) Heynh.. We report here the cloning of the AGL21 MADS-box gene, which belongs to the ANR1 clade, and the mRNA in situ expression patterns of this and two other root MADS-box genes. AGL17 appears to be a lateral root cap marker in the root tip, and towards the elongation zone this gene is expressed in the epidermal cells. AGL21 is highly expressed in lateral root primordia and it has a punctate expression pattern in the primary root meristem. AGL12 also has a punctate expression pattern in the primary root meristem. AGL12 and AGL21 are also expressed in the central cylinder of differentiated roots and both are expressed in developing embryos. This study, combined with previous phylogenetic analyses, indicates that these MADS-box genes may play distinct regulatory roles during root development.

Arabidopsis↗

Kinematic cues in perceptual weight judgement and their origins in box lifting.

When accepting a parcel from another person, we are able to use information about that person's movement to estimate in advance the weight of the parcel, that is, to judge its weight from observed action. Perceptual weight judgment provides a powerful method to study our interpretation of other people's actions, but it is not known what sources of information are used in judging weight. We have manipulated full form videos to obtain precise control of the perceived kinematics of a box lifting action, and use this technique to explore the kinematic cues that affect weight judgment. We find that observers rely most on the duration of the lifting movement to judge weight, and make less use of the durations of the grasp phase, when the box is first gripped, or the place phase, when the box is put down. These findings can be compared to the kinematics of natural box lifting behaviour, where we find that the duration of the grasp component is the best predictor of true box weight. The lack of accord between the optimal cues predicted by the natural behaviour and the cues actually used in the perceptual task has implications for our understanding of action observation in terms of a motor simulation. The differences between perceptual and motor behaviour are evidence against a strong version of the motor simulation hypothesis.

Adolescent↗

Grey-box modelling of pharmacokinetic/pharmacodynamic systems.

Grey-box pharmacokinetic/pharmacodynamic (PK/PD) modelling is presented as a promising way of modelling PK/PD systems. The concept behind grey-box modelling is based on combining physiological knowledge along with information from data in the estimation of model parameters. Grey-box modelling consists of using stochastic differential equations (SDEs) where the stochastic term in the differential equations represents unknown or incorrectly modelled dynamics of the system. The methodology behind the grey-box PK/PD modelling framework for systematic model improvement is illustrated using simulated data and furthermore applied to Bergman's minimal model of glucose kinetics using clinical data from an intravenous glucose tolerance test (IVGTT). The grey-box estimates of the stochastic system noise parameters indicate that the glucose minimal model is too simple and should preferably be revised in order to describe the complicated in vivo system of insulin and glucose following an IVGTT.

Blood Glucose↗

The same nuclear proteins bind the proximal CACCC box of the human beta-globin promoter and a similar sequence in the enhancer.

Using in vitro assays, we show that nuclear proteins related to the Sp1 and GT-1 factors bind to a CACCC box sequence in the human beta-globin enhancer, adjacent to binding sites for the erythroid-specific factor NFE1 and the ubiquitous factor CP1. The same proteins are known to bind to the proximal, but not to the distal, CACCC, box in the human beta-globin promoter. A C G mutation in the promoter CACCC box, known to cause beta-thalassemia, greatly decreases protein binding to the CACCC box; the same effect is obtained when this mutation is introduced into the enhancer CACCC box.

Base Sequence↗

A human B-box-binding protein downregulated in adenovirus 5-transformed human cells.

Internal promoters of some genes transcribed by RNA polymerase III (e.g. tRNA genes, adenovirus VA1 RNA gene, human retroposons of the Alu family) contain a conserved sequence element, B-box, interacting with basal transcription factor TFIIIC2 which initiates assembly of the full transcription complex on the genes, and which represents the major determinant of the efficiency of their expression. In this study we have identified in human nuclear extracts a protein which interacts with VA1 B-box DNA and forms a high-affinity complex which is very stable after the addition of a large excess of competitor DNA. Unlike TFIIIC2, the B-box-binding activity of the B-box-binding protein is found to be decreased in adenovirus 5-transformed human cells. In these cells (line 293) increased transcription of VA1 and tRNA genes in vivo and in vitro was previously detected by other workers. Our results suggest that besides TFIIIC2, an additional B-box-binding protein factor may be involved in the regulation of expression of the RNA polymerase III-transcribed genes.

Adenoviruses, Human↗

Functional analysis of Box II mutations in yeast site-specific recombinases Flp and R. Significance of amino acid conservation within the Int family and the yeast sub-family.

The site-specific recombinases Flp and R from Saccharomyces cerevisiae and Zygosaccharomyces rouxii, respectively, are related proteins that share approximately 30% amino acid matches. They exhibit a common reaction mechanism that appears to be conserved within the larger Integrase family of site-specific recombinases. Two regions of the proteins, designated as Box I and Box II, harbor, in addition to amino acid conservation, a significantly high degree of nucleotide sequence homology within their coding segments. Box II also contains two amino acids, a histidine and an arginine, that are invariant throughout the Int family. We have performed functional analysis of Flp and R variants carrying point mutations within the Box II segment. Several positions within Box II can tolerate substitutions with no effect, or only modest effects on recombination. Alterations of the Int family residues, His305 and Arg308, in the R protein lead to the arrest of recombination at the strand cleavage or the strand exchange step. This is very similar to previously observed "step-arrest" phenotypes in Flp variants altered at these positions and has strong implications for the catalytic mechanism of recombination. Flp and R variants at His305 and His309 can be complemented in half-site strand transfer by a corresponding Tyr343 to phenylalanine variant. In contrast to Arg308 Flp variants, which are efficiently complemented in half-site strand transfer by Flp(Y343F), no strong complementation has been observed between Arg308 variants of R and R (Y343F).

DNA Mutational Analysis↗

Effects of detention and illumination on rats' exploratory behavior in a two-box apparatus.

The effects of detention and lighting intensity on the exploratory behavior of male Wistar rats have been investigated by means of several types of two-box apparatus. Experiments consisted of six consecutive daily trials. Step-through latency values were taken up to 180 sec. Even a very short detention (10 sec) within the starting box exerted a powerful inhibitory influence on the exploratory behavior of the subjects. Uniformly well-lighted surroundings (both boxes) exerted an equally powerful inhibitory influence on the same behavior. This inhibition was only slightly decreased by the availability of visual cues. Only in the apparatus in which at least one box was dark was the exploratory behavior well maintained. Both detention and bright lighting inhibited selectively the exploratory, locomotor behavior of these animals and did not inhibit other motor activities. In fact, groomings and attempts (abortive passages from one box into the other) were repeatedly performed during the increased step-through latency. These activities are discussed as indicators of a conflict between drives.

Animals↗

Reliability of two activity boxes commonly used to assess drug induced behavioural changes.

Rats were given different drug treatments known to affect central catecholamine neurotransmission and to induce different types of behavioural changes which were recorded simultaneously by two different types of conventional activity boxes: an Animex activity meter and a photocell cage. All animals were also visually observed simultaneously with the automatic recordings. It was found that the two activity boxes reflected the behavioural changes differently and that the results from the two boxes were not correlated. When comparing the observations with the automatic recordings it was found that some clearly observable changes in behaviour were not reflected as changes in the automatic recordings and conversely that increases or decreases in the recorded motor activity were not always related to any particular changes in behaviour. The results show that motor activity can not be regarded as a simple or homogeneous behaviour that is reliably measured in conventional activity boxes. It is an undescriptive measure consisting of an artificial summation of those components of behaviour that affect the movement-detecting device in the particular box which is used. Practical and theoretical implications of this are discussed.

Animals↗

Homeo box genes of the Antennapedia and bithorax complexes of Drosophila.

The Antennapedia, Ultrabithorax, and fushi tarazu genes of Drosophila melanogaster each contain a very similar protein coding sequence, the homeo box. Previously cloned homeo box sequences were used to isolate additional well conserved members of the homeo box gene family. The most strongly conserved members of the homeo box gene family map within either the Antennapedia or Bithorax gene complexes. The tissue distribution of transcripts encoded by the two rightmost homeo box genes of the Bithorax complex are compared with the iab-2 and iab-7 phenotypes.

Animals↗

Recognition of the TACTAAC box during mRNA splicing in yeast involves base pairing to the U2-like snRNA.

The U2 snRNP binds to the site of branch formation during splicing of mammalian pre-mRNA in vitro. In Saccharomyces cerevisiae the branch site is within the so-called TACTAAC box (UACUAAC box), an absolutely conserved intron sequence required for splicing. Based on the identification and sequence of a U2 analogue in yeast, a specific base pairing interaction between the UACUAAC box and a highly conserved region of this snRNA can be proposed. To test this hypothesis, we have taken advantage of two mutations constructed previously in the UACUAAC box of an actin-HIS4 fusion. These mutant strains were transformed with stable plasmids bearing U2-like snRNAs into which changes predicted to restore base pairing had been introduced. Allele-specific suppression of biological and biochemical phenotypes was observed in both cases. Recognition of the UACUAAC box thus relies, at least in part, on Watson-Crick base pairing with the yeast U2 analogue.

Alleles↗

Chimeric reverse transcriptase of Moloney murine leukaemia virus, having the YXDD box of a Drosophila retrotransposon, 17.6.

All reverse transcriptases (RTs) so far examined are known to possess in common a stretch of 7 amino acids called the YXDD box. Various mutations were introduced in vitro into the nucleotide sequence coding for this box of Moloney murine leukaemia virus (Mo-MuLV) RT. The YXDD box of Mo-MuLV could be replaced by the counterpart of a Drosophila retrotransposon, 17.6, without loss of activity, while virtually complete loss of activity was detected in the case of replacement of the YXDD box of Rous sarcoma virus RT. Amino-acid substitution at position X resulted in significant change in divalent metal ion preference and enzyme activity, thus indicating that the YXDD box possibly constitutes a part of the active center of RT through metal ion binding.

Amino Acid Sequence↗

A cell type-specific silencer in the human choline acetyltransferase gene requiring two distinct and interactive E boxes.

We have previously reported that cholinergic neuron-specific expression of the human choline acetyltransferase gene is mediated by two co-operative silencers. We have now localized the proximal silencer to the region from nucleotide -2195 to -2409, which contains two distinct E boxes (CACCTG and CATGTG). Deletion or mutation of either of these E boxes results in a loss of silencer activity. There are specific nuclear proteins in adrenergic cells which bind to each of the two E boxes. However, nuclear proteins from cholinergic cells only bind the 5' E box not the 3' E box. It is this interaction which appears to be the cause of the inactivity of this silencer in these cells.

Base Sequence↗

Substance P antagonists block carbachol-induced "boxing" behavior at a site of coexistence in the rat prefrontal cortex.

A cholinergic projection from the dorsolateral tegmentum to the medial anterior cortex has previously been shown to contain substance P and corticotropin releasing factor. Behavioral analysis of acetylcholine, substance P and corticotropin releasing factor microinjected into the medial anterior cortex revealed a seizure-related "boxing" behavior elicited by carbachol, which was potentiated by coinjection with substance P and antagonized by coinjection with corticotropin releasing factor. We now report that two antagonists of substance P receptors, [D-Pro2, D-Phe7, D-Trp9]-substance P and [D-Pro2, D-Trp7,9]-substance P, attenuate "boxing" behavior when coinjected with carbachol. Neither antagonist produced observable behavioral effects when microinjected alone. An analog of substance P, [pGlu,5, MePhe,8 Sar9]-substance P (5-11) potentiated carbachol-induced "boxing" at doses similar to naturally-occurring substance P. Monoclonal and polyclonal antisera against substance P were not effective antagonists of carbachol-induced "boxing." The ability of substance P antagonists to block carbachol-induced "boxing" has two major implications: (1) endogenous substance P may be modulating endogenous acetylcholine in the tegmental-cortical pathway; and (2) substance P antagonists may provide a new avenue for the development of antiepileptic drugs.

Amino Acid Sequence↗